def get_restraint_values(threes):
res_type_group = get_res_type_group(threes[-2].resname, threes[-1].resname)
if res_type_group is None:
return None
restraint_values = []
key = threes.get_cdl_key(force_plus_one=True, omega_cdl=True)
previous_key = None
if len(key) == 4:
previous_key = key[:2]
key = key[-2:]
if previous_key:
rv = omega_database[res_type_group][previous_key]
restraint_values.append(rv)
else:
restraint_values.append(None)
rv = omega_database[res_type_group][key]
restraint_values.append(rv)
return restraint_values
def get_restraint_values(threes, interpolate=False):
from mmtbx.conformation_dependent_library import utils
res_type_group = cdl_utils.get_res_type_group(
threes[1].resname,
threes[2].resname,
)
if res_type_group is None: return None
if interpolate:
restraint_values = ["2", -1]
key = threes.get_cdl_key(exact=interpolate)
for i in range(2,26):
grid = utils.get_grid_values(res_type_group, key[0], key[1], column=i)
index = utils.get_index(*key)
r = utils.interpolate_2d(grid, index)
restraint_values.append(r)
else:
key = threes.get_cdl_key()
restraint_values = cdl_database[res_type_group][key]
return restraint_values
def test_cdl_lookup(hierarchy,
filename,
restraints_manager,
):
for i, threes in enumerate(cdl.generate_protein_threes(
hierarchy,
#restraints_manager=restraints_manager
geometry=restraints_manager.geometry,
)
):
res_type_group = cdl_utils.get_res_type_group(
threes[1].resname,
threes[2].resname,
)
key = threes.get_cdl_key(force_plus_one=True)
key = key[-2:]
restraint_values = omega_database[res_type_group][key]
print i, key, restraint_values[:4], filenames[filename][2]
del threes.registry.n
threes.registry.n = {}
assert restraint_values[:4] == filenames[filename][2][i]
def run2(args=(), out=sys.stdout):
argument_interpreter = libtbx.phil.command_line.argument_interpreter(
master_phil=master_phil,
home_scope="cdl_lookup")
phils = []
phil_args = []
pdbs = []
for arg in args:
if os.path.isfile(arg):
if iotbx.pdb.is_pdb_file(arg):
pdbs.append(arg)
continue
try :
file_phil = phil.parse(file_name=arg)
except RuntimeError :
pass
else :
phils.append(file_phil)
else :
phil_args.append(arg)
phils.append(argument_interpreter.process(arg))
working_phil = master_phil.fetch(sources=phils)
working_phil.show()
working_params = working_phil.extract()
if working_params.cdl_lookup.residue_group_class is None:
working_params.cdl_lookup.residue_group_class = cdl_utils.get_res_type_group(
*tuple(working_params.cdl_lookup.residue_names.split(",")[1:])
)
print "\nPeptide triplet class : %s" % working_params.cdl_lookup.residue_group_class
key = working_params.cdl_lookup.phi_psi_angles.split(",")
key[0] = int(key[0])
key[1] = int(key[1])
key = tuple(key)
restraints_values = cdl_database[working_params.cdl_lookup.residue_group_class][key]
outl = conformation_dependent_library.restraints_show(restraints_values)
print "\nCDL values\n%s" % outl
return restraints_values
def get_restraint_values(threes, interpolate=False):
from mmtbx.conformation_dependent_library import utils
res_type_group = cdl_utils.get_res_type_group(
threes[1].resname,
threes[2].resname,
)
if res_type_group is None: return None
if interpolate:
restraint_values = ["2", -1]
key = threes.get_cdl_key(exact=interpolate)
for i in range(2, 26):
grid = utils.get_grid_values(res_type_group,
key[0],
key[1],
column=i)
index = utils.get_index(*key)
r = utils.interpolate_2d(grid, index)
restraint_values.append(r)
else:
key = threes.get_cdl_key()
if key is None: return None
restraint_values = cdl_database[res_type_group][key]
return restraint_values
def run2(args=(), out=sys.stdout):
argument_interpreter = libtbx.phil.command_line.argument_interpreter(
master_phil=master_phil, home_scope="cdl_lookup")
phils = []
phil_args = []
pdbs = []
for arg in args:
if os.path.isfile(arg):
if iotbx.pdb.is_pdb_file(arg):
pdbs.append(arg)
continue
try:
file_phil = phil.parse(file_name=arg)
except RuntimeError:
pass
else:
phils.append(file_phil)
else:
phil_args.append(arg)
phils.append(argument_interpreter.process(arg))
working_phil = master_phil.fetch(sources=phils)
working_phil.show()
working_params = working_phil.extract()
if working_params.cdl_lookup.residue_group_class is None:
working_params.cdl_lookup.residue_group_class = cdl_utils.get_res_type_group(
*tuple(working_params.cdl_lookup.residue_names.split(",")[1:]))
print "\nPeptide triplet class : %s" % working_params.cdl_lookup.residue_group_class
key = working_params.cdl_lookup.phi_psi_angles.split(",")
key[0] = int(key[0])
key[1] = int(key[1])
key = tuple(key)
restraints_values = cdl_database[
working_params.cdl_lookup.residue_group_class][key]
outl = conformation_dependent_library.restraints_show(restraints_values)
print "\nCDL values\n%s" % outl
return restraints_values
def test_cdl_lookup(
hierarchy,
filename,
restraints_manager,
):
for i, threes in enumerate(
cdl.generate_protein_threes(
hierarchy,
#restraints_manager=restraints_manager
geometry=restraints_manager.geometry,
cdl_class=True,
)):
res_type_group = cdl_utils.get_res_type_group(
threes[1].resname,
threes[2].resname,
)
key = threes.get_cdl_key(force_plus_one=True)
key = key[-2:]
print('res_type_group', res_type_group, key)
restraint_values = omega_database[res_type_group][key]
print(i, key, restraint_values[:4], filenames[filename][2])
del threes.registry.n
threes.registry.n = {}
assert restraint_values[:4] == filenames[filename][2][i]
def get_restraint_values(threes):
res_type_group = get_res_type_group(
threes[-2].resname,
threes[-1].resname,
)
if res_type_group is None: return None
restraint_values = []
key = threes.get_cdl_key(force_plus_one=True,
omega_cdl=True,
)
if key is None: return None
previous_key = None
if len(key)==4:
previous_key = key[:2]
key = key[-2:]
if previous_key:
rv = omega_database[res_type_group][previous_key]
restraint_values.append(rv)
else:
restraint_values.append(None)
rv= omega_database[res_type_group][key]
restraint_values.append(rv)
return restraint_values
def get_restraint_values(threes,
cdl_svl=False,
interpolate=False):
from mmtbx.conformation_dependent_library import utils
res_type_group = cdl_utils.get_res_type_group(
threes[1].resname,
threes[2].resname,
)
if res_type_group is None: return None
#
if cdl_svl:
assert not interpolate
key = '%s/%s' % (['trans', 'cis'][threes.cis_group()],
['trans', 'cis'][threes.cis_group(omega_cdl=True)])
assert cdl_svl_database.get(key, None)
current = cdl_svl_database[key]
restraint_values = current[res_type_group]
return restraint_values
#
if threes.cis_group():
resnames = threes.get_resnames()
if resnames[1]=='PRO':
# cis-PRO
restraint_values = ['?', 0, 127.0, 2.4] # CNA
restraint_values += [102.6, 1.1, # NAB
112.1, 2.6, # NAC
112.0, 2.5, # BAC
120.2, 2.4, # ACO
117.1, 2.8, # ACN
121.1, 1.9, # OCN
1.338, 0.019, # CN
1.468, 0.017, # NA
1.533, 0.018, # AB
1.524, 0.020, # AC
1.228, 0.020, # CO
]
restraint_values += [120.6, 2.2, # CND
111.5, 1.4, # AND
103.8, 1.2, # NDG
104.0, 1.9, # ABG
105.4, 2.3, # BGD
1.506, 0.039, # BG
1.512, 0.027, # GD
1.474, 0.014, # ND
]
else:
# cis-NonPRO
restraint_values = ['?', 0, 123.0, 3.0]
return restraint_values
#
if interpolate:
restraint_values = ["2", -1]
key = threes.get_cdl_key(exact=interpolate)
for i in range(2,26):
grid = utils.get_grid_values(res_type_group, key[0], key[1], column=i)
index = utils.get_index(*key)
r = utils.interpolate_2d(grid, index)
restraint_values.append(r)
else:
key = threes.get_cdl_key()
if key is None: return None
restraint_values = cdl_database[res_type_group][key]
return restraint_values
